Genome of “potato famine” pathogen sequenced

CORVALLIS, Ore. – A large team of researchers has successfully sequenced the entire genome of one of the most famous pathogens in world history – which caused the Irish potato famine in the 1840s – in work that could ultimately help address a resurgence of this pathogen that is still causing almost $7 billion dollars of agricultural losses annually around the world.

Completion of the project, announced today in the journal Nature, is an important advance that could lead to new avenues of attack on this destructive pathogen, experts say. The work was led by the Broad Institute of Harvard University and MIT, and included collaborators from dozens of other institutions to make a task of this magnitude possible.

“Scientists have studied this pathogen for 150 years and there’s still a great deal we don’t know about it,” said James Carrington, professor and director of the Center for Genome Research and Biocomputing at Oregon State University and collaborator on the project. “It caused one of the most important famines in history and is still a major problem that costs billions of dollars to fight.”

In the short term, Carrington said, studies based on the new genetic “map” may help explain why the pathogen has been so aggressive, virulent and persistent, despite efforts to breed resistance to it. In the long run, the ability to breed far better plants and reduce use of chemicals will benefit from knowing exactly what genetic traits to look for and where they may be found on the huge genome of this pathogen, which has 240 million “base pairs” of DNA.

The pathogen, Phytophthora infestans, is commonly known as “late blight” and can infect potatoes, tomatoes and some other plants. Through its history it has been responsible for many crop epidemics, not the least of which was the Irish potato famine that led to the death of more than one million people in Ireland and a huge wave of immigration to the United States.

“This is probably the most costly plant pathogen, per acre, that we’ve ever had to deal with,” said Nik Grunwald, a plant pathologist with the USDA’s Agricultural Research Service and a courtesy associate professor of plant pathology at OSU. “Part of the problem is that we’ve identified and can grow potatoes with resistance to late blight, but they aren’t the varieties that the marketplace expects.”

The vast majority of potatoes consumed around the world are still russet potatoes that are inexpensive and highly popular, prized for the long, golden french fries they can produce – and extremely vulnerable to this pathogen, Grunwald said. But even with this pathogen to battle, potatoes are an important alternative to cereal crops and the fourth largest food crop in the world.

“We have some potato varieties that are completely resistant to late blight,” Grunwald said, “but most farmers are still growing russets because that’s where the demand is, even if they have to use up to 15 chemical sprays a season to produce them.”

According to Carrington, the genome of P. infestans is unusual, with long stretches of “repetitive DNA” that comprise almost 75 percent of its genome and play some role in its virulence and ability to adapt so rapidly to new environments. Many plants have evolved mechanisms for pathogen resistance, but this pathogen appears to tap into this odd, but massive collage of highly-repeated genome segments to overwhelm those defenses.

“These long sequences of repeating DNA contain virulence determinants, and those provide the ability for Phytophthora to change and adapt so readily to plant defenses,” Carrington said. “We believe it’s the key to the pathogen’s virulence.”

Researchers in Oregon, at both OSU and the USDA, will use their expertise in gene “silencing” – understanding what controls the genes that are activated and what turns them off - as a key part of their effort to decipher the secrets of this pathogen. Other researchers around the nation will continue work to learn about the basic biology and pathology of late blight.

“We’ve made great strides in recent years to do genome sequencing, it’s now becoming almost routine,” Carrington said. “But for these large projects we’re combining the use of powerful computers with teams of chemists, computational scientists, plant pathologists and many other experts to accomplish something that would take a smaller research group a lifetime.”

The researchers said in their report that “P. infestans remains a critical threat to world food security, and the genome sequence is a key tool to understanding its pathogenic success.”

Just this year, an outbreak of late blight has caused unusually early and severe damage to tomato and potato crops in the eastern United States. It’s difficult to control even with applications of fungicides, experts say, and can kill plants faster than almost any other disease.

In the mid-1990s, new and exotic strains of P. infestans made news headlines around the world. Particularly in the U.S. and Canada, the new strains appeared to be as or more pathogenic than any known previous strains, including those that caused the Irish potato famine.

Additional chemical treatments were routinely used and made it clear that, after more than a century, this pathogen has lost none of its virulence. The Oregon researchers believe that the new genome knowledge will accelerate development of chemical-free control methods.

This research was supported by the USDA and the National Science Foundation.